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Xu Y, Li Y, Chen Y, Wang L, Xue B, Zhang X, Song W, Guo W, Wu W. Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships. Genes (Basel) 2024; 15:716. [PMID: 38927652 PMCID: PMC11202638 DOI: 10.3390/genes15060716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.
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Affiliation(s)
- Yufen Xu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Yongquan Li
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Yanzhao Chen
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Longyuan Wang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Bine Xue
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Xianzhi Zhang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wenpei Song
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Wu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
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Wang Y, Li X, Feng Y, Wang J, Zhang J, Liu Z, Wang H, Chen T, He W, Wu Z, Lin Y, Zhang Y, Li M, Chen Q, Zhang Y, Luo Y, Tang H, Wang X. Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3116. [PMID: 37687365 PMCID: PMC10490022 DOI: 10.3390/plants12173116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Xueou Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Rural Revitalization Service Center, Agricultural and Rural Bureau of Cuiping District Yibin City, Yibin 644000, China
| | - Juan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Tao Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China;
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Zhiwei Wu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
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Gao XF, Xiong XH, Boufford DE, Gao YD, Xu B, Zhang C. Phylogeny of the Diploid Species of Rubus (Rosaceae). Genes (Basel) 2023; 14:1152. [PMID: 37372332 DOI: 10.3390/genes14061152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.
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Affiliation(s)
- Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xian-Hua Xiong
- College of Life Science and Biotechnology, Mianyang Teachers' College, Mianyang 621000, China
| | - David E Boufford
- Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Yun-Dong Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Cheng Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202684. [PMID: 36297708 PMCID: PMC9609754 DOI: 10.3390/plants11202684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/12/2023]
Abstract
The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
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Affiliation(s)
- Md Mazharul Islam
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
- Research and Development, Horticultural Crop Breeding, Quality Feeds Limited, Dhaka 1230, Bangladesh
| | - Deen Mohammad Deepo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation (GCER), College of Engineering Science and Environment, The University of Newcastle, Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Abu Bakar Siddique
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Oliul Hassan
- Department of Ecology and Environmental System, College of Ecology and Environmental Sciences, Kyungpook National University, Sangju 37224, Korea
| | - Abu Bakar Siddique
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Narayan Chandra Paul
- Kumho Life Science Laboratory, Department of Integrative Food Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
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Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives. Genes (Basel) 2022; 13:genes13040641. [PMID: 35456447 PMCID: PMC9028240 DOI: 10.3390/genes13040641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution.
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Abstract
Hibiscus exhibits high variation in chromosome number both within and among species. The Hibiscus mutabilis L. karyotype was analyzed in detail using fluorescence in situ hybridization (FISH) with oligonucleotide probes for (AG3T3)3 and 5S rDNA, which were tested here for the first time. In total, 90 chromosomes were counted in prometaphase and metaphase, and all exhibited similarly intense (AG3T3)3 signals at both ends. (AG3T3)3 showed little variation and thus did not allow discrimination among H. mutabilis chromosomes, but its location at both ends confirmed the integrity of each chromosome, thus contributing to accurate counting of the numerous, small chromosomes. Oligo-5S rDNA marked the proximal/distal regions of six chromosomes: weak signals on chromosomes 7 and 8, slightly stronger signals on chromosomes 15 and 16, and very strong signals on chromosomes 17 and 18. Therefore, 5S rDNA could assist in chromosome identification in H. mutabilis. Metaphase chromosome lengths ranged from 3.00 to 1.18 μm, indicating small chromosomes. The ratios of longest to shortest chromosome length in prometaphase and metaphase were 2.58 and 2.54, respectively, indicating karyotype asymmetry in H. mutabilis. These results provide an exact chromosome number and a physical map, which will be useful for genome assembly and contribute to molecular cytogenetics in the genus Hibiscus.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Zhoujian He
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
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Carter KA, Liston A, Bassil NV, Alice LA, Bushakra JM, Sutherland BL, Mockler TC, Bryant DW, Hummer KE. Target Capture Sequencing Unravels Rubus Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:1615. [PMID: 31921259 PMCID: PMC6933950 DOI: 10.3389/fpls.2019.01615] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/15/2019] [Indexed: 05/09/2023]
Abstract
Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.
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Affiliation(s)
- Katherine A. Carter
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Nahla V. Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Lawrence A. Alice
- Department of Biology, Western Kentucky University, Bowling Green, KY, United States
| | - Jill M. Bushakra
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Brittany L. Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Todd C. Mockler
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Douglas W. Bryant
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Kim E. Hummer
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
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Physical Map of FISH 5S rDNA and (AG 3T 3) 3 Signals Displays Chimonanthus campanulatus R.H. Chang & C.S. Ding Chromosomes, Reproduces its Metaphase Dynamics and Distinguishes Its Chromosomes. Genes (Basel) 2019; 10:genes10110904. [PMID: 31703401 PMCID: PMC6895986 DOI: 10.3390/genes10110904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 12/25/2022] Open
Abstract
Chimonanthus campanulatus R.H. Chang & C.S. Ding is a good horticultural tree because of its beautiful yellow flowers and evergreen leaves. In this study, fluorescence in situ hybridization (FISH) was used to analyse mitotic metaphase chromosomes of Ch. campanulatus with 5S rDNA and (AG3T3)3 oligonucleotides. Twenty-two small chromosomes were observed. Weak 5S rDNA signals were observed only in proximal regions of two chromosomes, which were adjacent to the (AG3T3)3 proximal signals. Weak (AG3T3)3 signals were observed on both chromosome ends, which enabled accurate chromosome counts. A pair of satellite bodies was observed. (AG3T3)3 signals displayed quite high diversity, changing in intensity from weak to very strong as follows: far away from the chromosome ends (satellites), ends, subtelomeric regions, and proximal regions. Ten high-quality spreads revealed metaphase dynamics from the beginning to the end and the transition to anaphase. Chromosomes gradually grew larger and thicker into linked chromatids, which grew more significantly in width than in length. Based on the combination of 5S rDNA and (AG3T3)3 signal patterns, ten chromosomes were exclusively distinguished, and the remaining twelve chromosomes were divided into two distinct groups. Our physical map, which can reproduce dynamic metaphase progression and distinguish chromosomes, will powerfully guide cytogenetic research on Chimonanthus and other trees.
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Wang Y, Chen Q, Chen T, Zhang J, He W, Liu L, Luo Y, Sun B, Zhang Y, Tang HR, Wang XR. Allopolyploid origin in Rubus (Rosaceae) inferred from nuclear granule-bound starch synthase I (GBSSI) sequences. BMC PLANT BIOLOGY 2019; 19:303. [PMID: 31291892 PMCID: PMC6617891 DOI: 10.1186/s12870-019-1915-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 07/02/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malachobatus. However, it remains unclear to be auto- or allo- polyploid origin of polyploids in Rubus. We investigated the homoeologs and the structure of the GBSSI-1 (granule-bound starch synthase I) gene in 140 Rubus individuals representing 102 taxa in 17 (out of the total 24) subsections of 7 (total of 12) sections at different ploidy levels. RESULTS Based on the gene structure and sequence divergence, we defined three gene variants, GBSSI-1a, GBSSI-1b, and GBSSI-1c. When compared with GBSSI-1a, both GBSSI-1b and GBSSI-1c have a shorter fourth intron, and GBSSI-1c had an additional deletion in the fifth intron. For diploids, either GBSSI-1a or GBSSI-1b was detected in 56 taxa consisting of 82 individuals from sect. Idaeobatus, while both alleles existed in R. pentagonus and R. peltatus. Both homoeologs GBSSI-1a and GBSSI-1b were identified in 39 taxa (48 individuals) of Malachobatus polyploids. They were also observed in two sect. Dalibardastrum taxa, in one sect. Chamaebatus taxon, and in three taxa from sect. Cylactis. Interestingly, all three homoeologs were observed in the three tetraploid taxa. Phylogenetic trees and networks suggested two clades (I and II), corresponding to GBSSI-1a, and GBSSI-1b/1c sequences, respectively. GBSSI-1 homoeologs from the same polyploid individual were resolved in different well-supported clades, and some of these homoelogs were more closely related to homoelogs in other species than they were to each other. This implied that the homoeologs of these polyploids were donated by different ancestral taxa, indicating their allopolyploid origin. Two kinds of diploids hybridized to form most allotetraploid species. The early-divergent diploid species with GBSSI-1a or -1b emerged before polyploid formation in the evolutionary history of Rubus. CONCLUSION This study provided new insights into allopolyploid origin and evolution from diploid to polyploid within the genus Rubus at the molecular phylogenetic level, consistent with the taxonomic treatment by Yü et al. and Lu.
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Affiliation(s)
- Yan Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Tao Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lin Liu
- Xizang Agriculture and Animal Husbandry College, Linzhi, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Hao-Ru Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Rong Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China.
- College of Horticulture, Sichuan Agricultural University, Chengdu, China.
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Luo X, Liu J, Wang J, Gong W, Chen L, Wan W. FISH analysis of Zanthoxylum armatum based on oligonucleotides for 5S rDNA and (GAA) 6. Genome 2018; 61:699-702. [PMID: 30067086 DOI: 10.1139/gen-2018-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridization (FISH) using oligonucleotide probes for (GAA)6 (18 bp) and ribosomal DNA (rDNA) (5S rDNA, 41 bp) was applied to analyse Zanthoxylum armatum. (GAA)6 loci were detected on the pericentromeric regions of five chromosome pairs, and 5S rDNA loci were also detected on the pericentromeric regions of another two chromosome pairs. The densities and locations of (GAA)6 and 5S rDNA signals varied between individual chromosomes. High-intensity (GAA)6 signals were detected at the centromeres of two large and two smaller metacentric chromosomes. Relatively strong (GAA)6 signals were detected at the centromeres of two relatively small metacentric chromosomes, although strong 5S rDNA signals were detected at the centromeres of two additional smaller metacentric chromosomes. Weak (GAA)6 signals were detected at the centromeres of four large metacentric chromosomes, whereas weak 5S rDNA signals were detected at the centromeres of two smaller metacentric chromosomes. The remaining chromosomes exhibited no signals. Zanthoxylum armatum had 2n = ∼128. The lengths of the mitotic metaphase chromosomes ranged from 1.22 to 2.34 μm. Our results provide information that may be beneficial for future cytogenetic studies and could contribute to the physical assembly of the Zanthoxylum genome.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Jingyan Wang
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Wei Gong
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Liang Chen
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
| | - Wenlin Wan
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China.,College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, China
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Herklotz V, Kovařík A, Lunerová J, Lippitsch S, Groth M, Ritz CM. The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non-symmetrical meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:77-90. [PMID: 29385286 DOI: 10.1111/tpj.13843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 01/03/2018] [Accepted: 01/15/2018] [Indexed: 05/02/2023]
Abstract
Dogroses represent an exceptional system for studying the effects of genome doubling and hybridization: their asymmetrical meiosis enables recombination in bi-parentally inherited chromosomes but prevents it in maternally inherited ones. We employed fluorescent in situ hybridization, genome skimming, amplicon sequencing of genomic and cDNA as well as conventional cloning of nuclear ribosomal DNA in two phylogenetically distinct pentaploid (2n = 5x = 35) species, Rosa canina and Rosa inodora, and their naturally occurring reciprocal hybrids, Rosa dumalis (5x) and Rosa agrestis (5x, 6x). Both progenitor species differed in composition, meiotic behaviour and expression of rDNA loci: R. canina (five 18S and 5-8 5S loci) was dominated by the Canina ribotypes, but R. inodora (four 18S loci and 7-8 5S loci) by the Rubiginosa ribotype. The co-localized 5S/18S loci occurred on either bivalent-forming (R. canina) or univalent-forming (R. inodora) chromosomes. Ribosomal DNA loci were additively inherited; however, the Canina ribotypes were dominantly expressed, even in genotypes with relatively low copy number of these genes. Moreover, we observed rDNA homogenization towards the paternally transmitted Canina ribotype in 6x R. agrestis. The here-observed variation in arrangement and composition of rDNA types between R. canina and R. inodora suggests the involvement of different genomes in bivalent formation. This results supports the hypothesis that the asymmetrical meiosis arose at least twice by independent ancient hybridization events.
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Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Susan Lippitsch
- Department of Ecology and Environment Protection, University of Applied Sciences Zittau/Görlitz, Theodor-Körner-Allee 16, D-02763, Zittau, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745, Jena, Germany
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
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Danilova TV, Akhunova AR, Akhunov ED, Friebe B, Gill BS. Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:317-330. [PMID: 28776783 DOI: 10.1111/tpj.13657] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/21/2017] [Accepted: 07/31/2017] [Indexed: 05/19/2023]
Abstract
During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross-species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next-generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross-genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter- and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Alina R Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Wang Y, Chen Q, Chen T, Tang H, Liu L, Wang X. Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs. FRONTIERS IN PLANT SCIENCE 2016; 7:968. [PMID: 27446191 PMCID: PMC4925702 DOI: 10.3389/fpls.2016.00968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/16/2016] [Indexed: 05/09/2023]
Abstract
Rubus L. is a large and taxonomically complex genus, species of which exhibit apomixis, polyploidy, and frequent hybridization. Most of Chinese Rubus are assigned in two major sections, Idaeobatus and Malachobatus. To explore the phylogenetic relationships within Chinese Rubus, inferences upon three chloroplast DNA (rbcL, rpl20-rps12, and trnG-trnS), nuclear ribosomal ITS, and two low-copy nuclear markers (GBSSI-2 and PEPC) were deduced in 142 Rubus taxa from 17 subsections in 6 sections. nrITS and GBSSI-2 were the most informative among the six DNA regions assessed. Phylogenetic relationships within Rubus were well-resolved by combined nuclear datasets rather than chloroplast markers. The phylogenetic inferences strongly supported that section Idaeobatus was a polyphyletic group with four distant clades. All samples of sect. Malachobatus formed a monophyletic clade, in which R. tsangorum and R. amphidasys of sect. Dalibardastrum, and R. peltatus from subsection Peltati of sect. Idaeobatus were always nested. Rubus pentagonus (2n = 2x = 14) from subsect. Alpestres of sect. Idaeobatus was a sister group to the polyploid sect. Malachobatus, as well as the polytomy of three sect. Cyalctis members. This suggests that some polyploids of Malachobatus might originate from common ancestors, via polyploidization of hybrids between R. pentagonus and sect. Cylactis species. They had experienced species explosion in a short time. Section Dalibardastrum species have potential parental lineages from subsects. Moluccani and Stipulosi of sect. Malachobatus. Based on molecular phylogenies, we also provided recommendations for the taxonomic treatments of four taxa. In addition, our results showed certain incongruence between chloroplast and nuclear markers, which might be due to hybridization and introgression.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Tao Chen
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural UniversityChengdu, China
| | - Lin Liu
- Agricultural and Animal Husbandry College of Tibet UniversityLinzhi, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural UniversityChengdu, China
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